HHsearch alignment for GI: 254780334 and conserved domain: cd03240

>cd03240 ABC_Rad50 The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.
Probab=96.85  E-value=0.02  Score=37.25  Aligned_cols=62  Identities=8%  Similarity=0.222  Sum_probs=37.3

Q ss_pred             CCCCCEEEECHHHHHHHHHHCCCCCCHHHHHHHHHH-HHHHHHHCCCEEEEEEEECCCCCCCCHHHHHHHHHEEEEEECC
Q ss_conf             169828997216876654204455636799999999-9997530797899986303665433114578775302785155
Q gi|254780334|r  165 NEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQA-MIQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMVDAVLYFEGG  243 (479)
Q Consensus       165 ~~~~~~vVIDSIQtl~~~~~~s~~GsvsQvre~~~~-L~~~AK~~~i~vilighvTK~G~iAGp~~LeH~VD~vl~~ege  243 (479)
T Consensus       137 ~~~p~lllLDEPT----s~LD~-----~~~~~~l~~ll~~~~~~~~~tiIivtHd--------~e~~-~~aD~vv~i~kd  198 (204)
T cd03240         137 GSNCGILALDEPT----TNLDE-----ENIEESLAEIIEERKSQKNFQLIVITHD--------EELV-DAADHIYRVEKD  198 (204)
T ss_pred             HCCCCEEEEECCC----CCCCH-----HHHHHHHHHHHHHHHHCCCCEEEEEECC--------HHHH-HHCCEEEEEECC
T ss_conf             4599989981876----66997-----8999999999999985699899999449--------8999-849959999589


Q ss_pred             C
Q ss_conf             5
Q gi|254780334|r  244 T  244 (479)
Q Consensus       244 ~  244 (479)
T Consensus       199 G  199 (204)
T cd03240         199 G  199 (204)
T ss_pred             C
T ss_conf             8